Molecular genetic variation was examined within and among species of the rock-dwelling
cichlid fishes (mbuna) of Lake Malawi. Phylogenetic relationships among mbuna mitochondrial
DNA (mtDNA) haplotypes were estimated by using restriction-fragment-length polymorphisms.
The distribution of these lineages among mbuna species is of particular significance for
phylogenetic systematic study of this fauna. Some species were found to be polymorphic for
divergent haplotypes that substantially predate their isolation from sister taxa. Repeated
speciation events among numerous closely related taxa appear to have been so recent that
mtDNA lineage sorting among species is incomplete. Thus, the mtDNA gene tree is not congruent
with the putative species tree. These results indicate that analysis of mtDNA alone will not
be sufficient for resolution of phylogenetic relationships in the mbuna. Clarification of
these relationships will require examination of multiple nuclear loci, because many of these
new markers are also likely to retain ancestral polymorphisms.